Variant report

Variant	rs12600478
Chromosome Location	chr17:46163165-46163166
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46151032..46153908-chr17:46162151..46164546,2	MCF-7	breast:
2	chr17:46125259..46127124-chr17:46161475..46163962,3	MCF-7	breast:
3	chr17:46161644..46163852-chr17:46183835..46185644,2	MCF-7	breast:
4	chr17:46162883..46164611-chr17:46178466..46180431,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108468	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000263412	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10514935	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs12600464	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs1317850	0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs2240123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2938484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2957935	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs8076163	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	esv1804681	chr17:46144628-46168544	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
5	esv3517734	chr17:46158653-46163301	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3517735	chr17:46159053-46163301	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv3517736	chr17:46159053-46163301	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46139800-46163600	Weak transcription	Esophagus	oesophagus
2	chr17:46140800-46163200	Weak transcription	Colonic Mucosa	Colon
3	chr17:46143800-46163200	Weak transcription	Aorta	Aorta
4	chr17:46144800-46177800	Weak transcription	Right Ventricle	heart
5	chr17:46147800-46177600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr17:46149000-46178000	Weak transcription	Lung	lung
7	chr17:46152400-46168200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr17:46152400-46177200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr17:46152600-46176800	Weak transcription	K562	blood
10	chr17:46152600-46177000	Weak transcription	HSMMtube	muscle
11	chr17:46153400-46170800	Weak transcription	HSMM	muscle
12	chr17:46153800-46176800	Weak transcription	NHLF	lung
13	chr17:46154000-46163200	Weak transcription	Pancreas	Pancrea
14	chr17:46154200-46163200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr17:46154200-46163600	Weak transcription	NHDF-Ad	bronchial
16	chr17:46154200-46176800	Weak transcription	HMEC	breast
17	chr17:46154200-46177600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr17:46154400-46163200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr17:46154400-46163200	Weak transcription	Brain Angular Gyrus	brain
20	chr17:46154400-46163200	Weak transcription	Fetal Muscle Leg	muscle
21	chr17:46154400-46163200	Weak transcription	Left Ventricle	heart
22	chr17:46154400-46163200	Weak transcription	GM12878-XiMat	blood
23	chr17:46154400-46163400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr17:46154400-46166000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr17:46154400-46166000	Weak transcription	HUVEC	blood vessel
26	chr17:46154400-46166200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr17:46154400-46167800	Weak transcription	Primary B cells from cord blood	blood
28	chr17:46154400-46168000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr17:46154400-46170600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr17:46154400-46170800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr17:46154400-46170800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr17:46154400-46170800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr17:46154400-46171000	Weak transcription	HepG2	liver
34	chr17:46154400-46171200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr17:46154400-46171200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr17:46154400-46171200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr17:46154400-46171200	Weak transcription	Spleen	Spleen
38	chr17:46154400-46173000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr17:46154400-46176800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr17:46154400-46177000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr17:46154400-46177200	Weak transcription	Placenta	Placenta
42	chr17:46154400-46177600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr17:46154400-46177600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr17:46154400-46177600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr17:46154400-46177600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr17:46154400-46177600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr17:46154400-46177600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr17:46154400-46177800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr17:46154600-46163200	Weak transcription	NH-A	brain
50	chr17:46154600-46163400	Weak transcription	Muscle Satellite Cultured Cells	--

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